Merge branch 'master' into enh/MRTrix3

Author: oesteban

doc/quickstart.rst

@@ -50,3 +50,13 @@ Developer guides
    devel/gitwash/index
 
 .. include:: links_names.txt
+
+Useful links for beginners
+===========================
+
+Getting started with Python - Tutorials. `Available here`__
+
+Python for Beginners `Available here`__
+
+   __ http://www.codecademy.com/en/tracks/python
+   __ https://www.python.org/about/gettingstarted/

doc/users/tutorial_101.rst

@@ -99,15 +99,15 @@ This results in a workflow containing two isolated nodes:
 
 **5. Connecting nodes to each other**
 
-We want to connect the output produced by realignment to the input of
-smoothing. This is done as follows.
+We want to connect the output produced by the node realignment to the input of
+the node smoothing. This is done as follows.
 
 .. testcode::
 
    workflow.connect(realigner, 'realigned_files', smoother, 'in_files')
 
-or alternatively, a more flexible notation can be used. Although not shown here,
-the following notation can be used to connect multiple outputs from one node to
+
+Although not shown here, the following notation can be used to connect multiple outputs from one node to
 multiple inputs (see step 7 below).
 
 .. testcode::
@@ -189,3 +189,22 @@ inside which are three folders: realign, smooth and artdetect (the names
 of the nodes). The outputs of these routines are in these folders.
 
 .. include:: ../links_names.txt
+
+.. glossary::
+
+   pipeline
+      Connected series of processes (processes can be run parallel and or sequential)
+
+   workflow 
+      (kind of synonymous to pipeline) = hosting the nodes
+
+   node 
+      = switching-point within a pipeline, you can give it a name (in the above example e.g. realigner), 
+      a node usually requires an or several inputs and will produce an or several outputs
+
+   interface 
+      = specific software (e.g. FSL, SPM ...) are wrapped in interfaces, within a node instances of an
+      interface can be run
+
+   modules 
+      for each interface the according modules have to be imported in the usual pythonic manner

nipype/utils/nipype2boutiques.py

@@ -40,29 +40,27 @@ def print_inputs(tool_name, module=None, function=None):
         tool_outputs = []
 
         for name, spec in sorted(interface.inputs.traits(transient=None).items()):
-
-            #FIXME: optional inputs are not supported yet
-            if not ( hasattr(spec, "mandatory") and spec.mandatory ):
-                continue
 
             input = {}
+
             input['name'] = name
             type = spec.full_info(inputs, name, None)
-            if not "an existing file name" in type:
-                type = "String"
+            if "an existing file name" in type:
+                type = "File"
             else:
-                type = "File"            
+                type = "String"            
             input['type'] = type
             input['description'] = "\n".join(interface._get_trait_desc(inputs, name, spec))[len(name)+2:].replace("\n\t\t",". ")
             command_line_key = "["+str(input_counter)+"_"+name.upper()+"]"
             input_counter += 1
             input['command-line-key'] = command_line_key
             input['cardinality'] = "Single"
-            tool_inputs.append(input)
-            
-            if not ( hasattr(spec, "mandatory") and spec.mandatory ): 
-                command_line+= "--%s"%name+" "                        # unreachable code as long as optional inputs are not supported
+            if not ( hasattr(spec, "mandatory") and spec.mandatory ):
+                input['optional'] = "true"
+                input['command-line-flag'] = "--%s"%name+" "
 
+            tool_inputs.append(input)
+
             command_line+= command_line_key+" "
 
             # add value to input so that output names can be generated
@@ -89,8 +87,7 @@ def print_inputs(tool_name, module=None, function=None):
                 output['value-template'] = os.path.basename(output_value)
 
             output['cardinality'] = "Single"
-            if output['value-template'] != "": # outputs with no templates would certainly crash.
-              tool_outputs.append(output)
+            tool_outputs.append(output)
 
         # remove all temporary file names from inputs
         for input in tool_inputs:
@@ -101,7 +98,7 @@ def print_inputs(tool_name, module=None, function=None):
         tool_desc['command-line'] = command_line
         tool_desc['docker-image'] = 'docker.io/robdimsdale/nipype'
         tool_desc['docker-index'] = 'http://index.docker.io'
-        tool_desc['schema-version'] = '0.1'
+        tool_desc['schema-version'] = '0.2-snapshot'
         print json.dumps(tool_desc, indent=4, separators=(',', ': '))
 
 def main(argv):